The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment.

ABSTRACT:

Background

Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction. Currently, available tools provide different (sets of) constraints and default parameter sets. Thus, it is hard to impossible for users to estimate the influence of individual restrictions on the prediction results.

Results

Here, we present a systematic assessment of the impact of established and new constraints on sRNA target prediction both on a qualitative as well as computational level. This is done exemplarily based on the performance of IntaRNA, one of the most exact sRNA target prediction tools. IntaRNA provides various ways to constrain considered seed interactions, e.g. based on seed length, its accessibility, minimal

SUBMITTER: Raden M 

PROVIDER: S-EPMC6956497 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature